› 4oyt

X-ray diffraction
2.4Å resolution

Crystal structure of ternary complex of Plasmodium vivax SHMT with D-serine and folinic acid

Released:
DOI: 10.2210/pdb4oyt/pdb
PDB entry 4oyt coloured by chain, front view.
PDB entry 4oyt coloured by chain, side view.
PDB entry 4oyt coloured by chain, top view.
Source organism: Plasmodium vivax Sal-1
Primary publication:
Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control.
Chitnumsub P, Jaruwat A, Riangrungroj P, Ittarat W, Noytanom K, Oonanant W, Vanichthanankul J, Chuankhayan P, Maenpuen S, Chen CJ, Chaiyen P, Yuthavong Y, Leartsakulpanich U
Acta Crystallogr D Biol Crystallogr 70 3177-86 (2014)
PMID: 25478836

Function and Biology Details

Reaction catalysed: 
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107691 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
glycine hydroxymethyltransferase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 442 amino acids
Theoretical weight: 49.25 KDa
Source organism: Plasmodium vivax Sal-1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A5K8L9 (Residues: 1-442; Coverage: 100%)
Gene name: PVX_100730
Sequence domains: Serine hydroxymethyltransferase
Structure domains:

Ligands and Environments


Cofactor: Ligand FON 3 x FON
4 bound ligands:
Ligand 1W9 3 x 1W9
Ligand GOL 3 x GOL
Ligand TRS 1 x TRS
Ligand ETF 1 x ETF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: C2
Unit cell:
a: 100.619Å b: 58.115Å c: 236.614Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.2 0.252
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Artemisinin-based antimalarial research: application of biotechnology to the production of artemisinin, its mode of action, and the mechanism of resistance of Plasmodium parasites.
Muangphrom et al. (2016)
7 other articles

5 mentions without citation

Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control.
Chitnumsub et al. (2014)
4 more